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For our TMFs, we put a leading “1” for trial level; a leading “2” for country level and a leading “3” site. When we used to file paper we would have a set of folders at the Trial level and we would label, ex. 101.01.01 – TMF Plan. If country level applies to your study I would suggest doing a set of folders for each country participating. ex. 201.01.08 Monitoring Plan; and a set of folders for each site ex. 301.01.11 Debarment Statement.
You can certainly color code individual countries, or give them a country code. 01-US; 02-CAN; 03-UK; 04-EU, etc.
Hope this helps. This is how our eTMF is structured using the TMF RM.